ReaDDy - A Software for Particle-Based Reaction-Diffusion Dynamics in Crowded Cellular Environments

被引:100
作者
Schoeneberg, Johannes [1 ]
Noe, Frank [1 ]
机构
[1] Free Univ Berlin, Dept Math, Berlin, Germany
来源
PLOS ONE | 2013年 / 8卷 / 09期
关键词
BROWNIAN DYNAMICS; SECRETORY GRANULES; MOLECULAR-DYNAMICS; SIMULATIONS; RHODOPSIN; MEMBRANE; ALGORITHMS; MICROSCOPY; BIOLOGY; SPACE;
D O I
10.1371/journal.pone.0074261
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
We introduce the software package ReaDDy for simulation of detailed spatiotemporal mechanisms of dynamical processes in the cell, based on reaction-diffusion dynamics with particle resolution. In contrast to other particle-based reaction kinetics programs, ReaDDy supports particle interaction potentials. This permits effects such as space exclusion, molecular crowding and aggregation to be modeled. The biomolecules simulated can be represented as a sphere, or as a more complex geometry such as a domain structure or polymer chain. ReaDDy bridges the gap between small-scale but highly detailed molecular dynamics or Brownian dynamics simulations and large-scale but little-detailed reaction kinetics simulations. ReaDDy has a modular design that enables the exchange of the computing core by efficient platform-specific implementations or dynamical models that are different from Brownian dynamics.
引用
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页数:14
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